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Gunawardena HP, Jayatilake MM, Brelsford JD, Nanda H. Diagnostic utility of N-terminal TMPP labels for unambiguous identification of clipped sites in therapeutic proteins. Sci Rep 2023; 13:18602. [PMID: 37903854 PMCID: PMC10616084 DOI: 10.1038/s41598-023-45446-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/19/2023] [Indexed: 11/01/2023] Open
Abstract
Protein therapeutics are susceptible to clipping via enzymatic and nonenzymatic mechanisms that create neo-N-termini. Typically, neo-N-termini are identified by chemical derivatization of the N-terminal amine with (N-Succinimidyloxycarbonylmethyl)tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP) followed by proteolysis and mass spectrometric analysis. Detection of the TMPP-labeled peptide is achieved by mapping the peptide sequence to the product ion spectrum derived from collisional activation. The site-specific localization of the TMPP tag enables unambiguous determination of the true N-terminus or neo-N-termini. In addition to backbone product ions, TMPP reporter ions at m/z 573, formed via collision-induced dissociation, can be diagnostic for the presence of a processed N-termini. However, reporter ions generated by collision-induced dissociation may be uninformative because of their low abundance. We demonstrate a novel high-throughput LC-MS method for the facile generation of the TMPP reporter ion at m/z 533 and, in some instances m/z 590, upon electron transfer dissociation. We further demonstrate the diagnostic utility of TMPP labeled peptides derived from a total cell lysate shows high degree of specificity towards selective N-terminal labeling over labeling of lysine and tyrosine and highly-diagnostic Receiver Operating Characteristic's (ROC) of TMPP reporter ions of m/z 533 and m/z 590. The abundant generation of these reporters enables subsequent MS/MS by intensity and m/z-dependent triggering of complementary ion activation modes such as collision-induced dissociation, high-energy collision dissociation, or ultraviolet photo dissociation for subsequent peptide sequencing.
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Affiliation(s)
- Harsha P Gunawardena
- Janssen Research and Development LLC, The Janssen Pharmaceutical Companies of Johnson & Johnson, Spring House, PA, USA.
| | - Meth M Jayatilake
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | - Jeffery D Brelsford
- Janssen Research and Development LLC, The Janssen Pharmaceutical Companies of Johnson & Johnson, Spring House, PA, USA
| | - Hirsh Nanda
- Janssen Research and Development LLC, The Janssen Pharmaceutical Companies of Johnson & Johnson, Spring House, PA, USA
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2
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Wang R, Wang Z, Lu H. Separation methods for system-wide profiling of protein terminome. Proteomics 2023; 23:e2100374. [PMID: 35997653 DOI: 10.1002/pmic.202100374] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 08/07/2022] [Accepted: 08/09/2022] [Indexed: 11/10/2022]
Abstract
Protein N- and C-termini have specific biochemical properties and functions. They play vital roles in various biological processes, such as protein stability and localization. In addition, post-translational modifications and proteolytic processing generate different proteoforms at protein termini. In recent years, terminomics has attracted significant attention, and numerous strategies have been developed to achieve high-throughput and global terminomics analysis. This review summarizes the recent protein N-termini and C-termini enrichment methods and their application in different samples. We also look ahead further application of terminomics in profiling protease substrates and discovery of disease biomarkers and therapeutic targets.
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Affiliation(s)
- Rui Wang
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China
| | - Zhongjie Wang
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China
| | - Haojie Lu
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China.,Department of Chemistry and Key Laboratory of Glycoconjugates Research Ministry of Public Health, Fudan University, Shanghai, People's Republic of China
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3
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Koudelka T, Winkels K, Kaleja P, Tholey A. Shedding light on both ends: An update on analytical approaches for N- and C-terminomics. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1869:119137. [PMID: 34626679 DOI: 10.1016/j.bbamcr.2021.119137] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/27/2021] [Accepted: 09/06/2021] [Indexed: 02/04/2023]
Abstract
Though proteases were long regarded as nonspecific degradative enzymes, over time, it was recognized that they also hydrolyze peptide bonds very specifically with a limited substrate pool. This irreversible posttranslational modification modulates the fate and activity of many proteins, making proteolytic processing a master switch in the regulation of e.g., the immune system, apoptosis and cancer progression. N- and C-terminomics, the identification of protein termini, has become indispensable in elucidating protease substrates and therefore protease function. Further, terminomics has the potential to identify yet unknown proteoforms, e.g. formed by alternative splicing or the recently discovered alternative ORFs. Different strategies and workflows have been developed that achieve higher sensitivity, a greater depth of coverage or higher throughput. In this review, we summarize recent developments in both N- and C-terminomics and include the potential of top-down proteomics which inherently delivers information on both ends of analytes in a single analysis.
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Affiliation(s)
- Tomas Koudelka
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Konrad Winkels
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Patrick Kaleja
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Andreas Tholey
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany.
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4
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Bagal D, Gibson BW. Identification of Proteolysis Products in Protein Therapeutics through TMPP N-Terminal Tagging and Electron Transfer Dissociation Product Triggered Collisional Induced Dissociation Fragmentation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1936-1944. [PMID: 33534996 DOI: 10.1021/jasms.0c00391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Thorough characterization of protein therapeutics is often challenging due to the heterogeneity arising from primary sequence variants, post-translational modifications, proteolytic clipping, or incomplete processing of the signal peptide. Modern mass spectrometry (MS) techniques are now routinely used to characterize such heterogeneous protein populations. Here, we present an LC-MS/MS method using (N-succinimidyloxycarbonylmethyl)-tris (2,4,6-trimethoxyphenyl) phosphonium bromide (TMPP-Ac-OSu) to label any free N-terminal α-amines to rapidly and selectively identify proteolytic clipping events. Electron transfer dissociation (ETD) fragmentation of these chemically tagged peptides generates two unique TMPP product ions, TMPP+ and TMPP-Ac-NH2/c0. The presence of these signature ions following ETD is used to trigger subsequent collisional induced dissociation (CID) fragmentation of the precursor ion. This results in a small subset of CID tandem MS spectra that are used in a customized database search. Using a purified fusion monoclonal antibody (mAb) as an example, we demonstrate how TMPP labeling followed by ETD product ion triggered CID fragmentation is used to accurately identify two undesired clipping sites.
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Affiliation(s)
- Dhanashri Bagal
- Amgen Discovery Research, Discovery Attribute Sciences, South San Francisco, California 94080, United States
| | - Bradford W Gibson
- Amgen Discovery Research, Discovery Attribute Sciences, South San Francisco, California 94080, United States
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5
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Kaushal P, Lee C. N-terminomics - its past and recent advancements. J Proteomics 2020; 233:104089. [PMID: 33359939 DOI: 10.1016/j.jprot.2020.104089] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 07/22/2020] [Accepted: 12/20/2020] [Indexed: 02/06/2023]
Abstract
N-terminomics is a rapidly evolving branch of proteomics that encompasses the study of protein N-terminal sequence. A proteome-wide collection of such sequences has been widely used to understand the proteolytic cascades and in annotating the genome. Over the last two decades, various N-terminomic strategies have been developed for achieving high sensitivity, greater depth of coverage, and high-throughputness. We, in this review, cover how the field of N-terminomics has evolved to date, including discussion on various sample preparation and N-terminal peptide enrichment strategies. We also compare different N-terminomic methods and highlight their relative benefits and shortcomings in their implementation. In addition, an overview of the currently available bioinformatics tools and data analysis pipelines for the annotation of N-terminomic datasets is also included. SIGNIFICANCE: It has been recognized that proteins undergo several post-translational modifications (PTM), and a number of perturbed biological pathways are directly associated with modifications at the terminal sites of a protein. In this regard, N-terminomics can be applied to generate a proteome-wide landscape of mature N-terminal sequences, annotate their source of generation, and recognize their significance in the biological pathways. Besides, a system-wide study can be used to study complicated proteolytic machinery and protease cleavage patterns for potential therapeutic targets. Moreover, due to unprecedented improvements in the analytical methods and mass spectrometry instrumentation in recent times, the N-terminomic methodologies now offers an unparalleled ability to study proteoforms and their implications in clinical conditions. Such approaches can further be applied for the detection of low abundant proteoforms, annotation of non-canonical protein coding sites, identification of candidate disease biomarkers, and, last but not least, the discovery of novel drug targets.
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Affiliation(s)
- Prashant Kaushal
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Republic of Korea
| | - Cheolju Lee
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Republic of Korea; KHU-KIST Department of Converging Science and Technology, Kyung Hee University, 26 Kyunghee-daero, Dongdaemun-gu, Seoul 02447, Republic of Korea.
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6
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Sun M, Liang Y, Li Y, Yang K, Zhao B, Yuan H, Li X, Zhang X, Liang Z, Shan Y, Zhang L, Zhang Y. Comprehensive Analysis of Protein N-Terminome by Guanidination of Terminal Amines. Anal Chem 2019; 92:567-572. [DOI: 10.1021/acs.analchem.9b04141] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mingwei Sun
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, Guangdong 510005, China
| | - Yu Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Yang Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kaiguang Yang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Baofeng Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Huiming Yuan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Xiao Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Xiaodan Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Zhen Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Yichu Shan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
| | - Yukui Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning 116023, China
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7
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Li L, Yan G, Zhang X. A rapid and efficient method for N-termini analysis in short-lived proteins. Talanta 2019; 204:367-371. [DOI: 10.1016/j.talanta.2019.06.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 06/02/2019] [Accepted: 06/08/2019] [Indexed: 02/05/2023]
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8
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9
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Leitner A. A review of the role of chemical modification methods in contemporary mass spectrometry-based proteomics research. Anal Chim Acta 2018; 1000:2-19. [DOI: 10.1016/j.aca.2017.08.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 07/11/2017] [Accepted: 08/15/2017] [Indexed: 12/20/2022]
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10
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Klein T, Eckhard U, Dufour A, Solis N, Overall CM. Proteolytic Cleavage-Mechanisms, Function, and "Omic" Approaches for a Near-Ubiquitous Posttranslational Modification. Chem Rev 2017; 118:1137-1168. [PMID: 29265812 DOI: 10.1021/acs.chemrev.7b00120] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Proteases enzymatically hydrolyze peptide bonds in substrate proteins, resulting in a widespread, irreversible posttranslational modification of the protein's structure and biological function. Often regarded as a mere degradative mechanism in destruction of proteins or turnover in maintaining physiological homeostasis, recent research in the field of degradomics has led to the recognition of two main yet unexpected concepts. First, that targeted, limited proteolytic cleavage events by a wide repertoire of proteases are pivotal regulators of most, if not all, physiological and pathological processes. Second, an unexpected in vivo abundance of stable cleaved proteins revealed pervasive, functionally relevant protein processing in normal and diseased tissue-from 40 to 70% of proteins also occur in vivo as distinct stable proteoforms with undocumented N- or C-termini, meaning these proteoforms are stable functional cleavage products, most with unknown functional implications. In this Review, we discuss the structural biology aspects and mechanisms of catalysis by different protease classes. We also provide an overview of biological pathways that utilize specific proteolytic cleavage as a precision control mechanism in protein quality control, stability, localization, and maturation, as well as proteolytic cleavage as a mediator in signaling pathways. Lastly, we provide a comprehensive overview of analytical methods and approaches to study activity and substrates of proteolytic enzymes in relevant biological models, both historical and focusing on state of the art proteomics techniques in the field of degradomics research.
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Affiliation(s)
- Theo Klein
- Life Sciences Institute, Department of Oral Biological and Medical Sciences, and ‡Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, British Columbia V6T 1Z4, Canada
| | - Ulrich Eckhard
- Life Sciences Institute, Department of Oral Biological and Medical Sciences, and ‡Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, British Columbia V6T 1Z4, Canada
| | - Antoine Dufour
- Life Sciences Institute, Department of Oral Biological and Medical Sciences, and ‡Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, British Columbia V6T 1Z4, Canada
| | - Nestor Solis
- Life Sciences Institute, Department of Oral Biological and Medical Sciences, and ‡Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, British Columbia V6T 1Z4, Canada
| | - Christopher M Overall
- Life Sciences Institute, Department of Oral Biological and Medical Sciences, and ‡Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, British Columbia V6T 1Z4, Canada
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11
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Marshall NC, Finlay BB, Overall CM. Sharpening Host Defenses during Infection: Proteases Cut to the Chase. Mol Cell Proteomics 2017; 16:S161-S171. [PMID: 28179412 PMCID: PMC5393396 DOI: 10.1074/mcp.o116.066456] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 02/03/2017] [Indexed: 01/14/2023] Open
Abstract
The human immune system consists of an intricate network of tightly controlled pathways, where proteases are essential instigators and executioners at multiple levels. Invading microbial pathogens also encode proteases that have evolved to manipulate and dysregulate host proteins, including host proteases during the course of disease. The identification of pathogen proteases as well as their substrates and mechanisms of action have empowered significant developments in therapeutics for infectious diseases. Yet for many pathogens, there remains a great deal to be discovered. Recently, proteomic techniques have been developed that can identify proteolytically processed proteins across the proteome. These “degradomics” approaches can identify human substrates of microbial proteases during infection in vivo and expose the molecular-level changes that occur in the human proteome during infection as an operational network to develop hypotheses for further research as well as new therapeutics. This Perspective Article reviews how proteases are utilized during infection by both the human host and invading bacterial pathogens, including archetypal virulence-associated microbial proteases, such as the Clostridia spp. botulinum and tetanus neurotoxins. We highlight the potential knowledge that degradomics studies of host–pathogen interactions would uncover, as well as how degradomics has been successfully applied in similar contexts, including use with a viral protease. We review how microbial proteases have been targeted in current therapeutic approaches and how microbial proteases have shaped and even contributed to human therapeutics beyond infectious disease. Finally, we discuss how, moving forward, degradomics research can greatly contribute to our understanding of how microbial pathogens cause disease in vivo and lead to the identification of novel substrates in vivo, and the development of improved therapeutics to counter these pathogens.
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Affiliation(s)
- Natalie C Marshall
- From the ‡Department of Microbiology & Immunology.,§Michael Smith Laboratories
| | - B Brett Finlay
- From the ‡Department of Microbiology & Immunology.,§Michael Smith Laboratories.,¶Department of Biochemistry & Molecular Biology
| | - Christopher M Overall
- ¶Department of Biochemistry & Molecular Biology, .,**Department of Oral Biological & Medical Sciences, Centre for Blood Research, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
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12
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Abstract
Omics approaches have become popular in biology as powerful discovery tools, and currently gain in interest for diagnostic applications. Establishing the accurate genome sequence of any organism is easy, but the outcome of its annotation by means of automatic pipelines remains imprecise. Some protein-encoding genes may be missed as soon as they are specific and poorly conserved in a given taxon, while important to explain the specific traits of the organism. Translational starts are also poorly predicted in a relatively important number of cases, thus impacting the protein sequence database used in proteomics, comparative genomics, and systems biology. The use of high-throughput proteomics data to improve genome annotation is an attractive option to obtain a more comprehensive molecular picture of a given organism. Here, protocols for reannotating prokaryote genomes are described based on shotgun proteomics and derivatization of protein N-termini with a positively charged reagent coupled to high-resolution tandem mass spectrometry.
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13
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Chen L, Shan Y, Weng Y, Sui Z, Zhang X, Liang Z, Zhang L, Zhang Y. Hydrophobic Tagging-Assisted N-Termini Enrichment for In-Depth N-Terminome Analysis. Anal Chem 2016; 88:8390-5. [DOI: 10.1021/acs.analchem.6b02453] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Lingfan Chen
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yichu Shan
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Yejing Weng
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Zhigang Sui
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Xiaodan Zhang
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Zhen Liang
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Lihua Zhang
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Yukui Zhang
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
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14
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Armengaud J. Power of positive thinking in quantitative proteomics. Proteomics 2016; 15:2898-900. [PMID: 26227558 DOI: 10.1002/pmic.201500307] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 07/24/2015] [Indexed: 01/20/2023]
Abstract
Derivatization of proteins with specific isotope reagents has been widely explored for quantitative proteomics where the relative abundances of proteins present in different complex samples are compared by MS. This represents an interesting arena for innovation, where protein chemistry and MS are associated for the best of both worlds. Among the numerous reagents developed, those that introduce a permanent positive charge, such as (N-succinimidyloxycarbonylmethyl)-tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP), increase the ionizability of their targets and thus improve the sensitivity of the approach. TMPP labeling also modifies the hydrophobicity and changes the peptide fragmentation pattern. Because TMPP reacts preferably with the N-termini of proteins and peptides, its use has been explored for proteogenomics and de novo protein sequencing. In this issue of Proteomics, Shen et al. (Proteomics 2015, 15, 2903-2909) show that accurate quantitation of proteins can be obtained with light/heavy TMPP-labeling of peptides, which can be easily prepared and desalted in a homemade C8-SCX-C8 stagetip, and then monitored by nano-LC-MS/MS analysis. Their results demonstrate enhanced sequence coverage compared with other approaches. Combined with an efficient enrichment procedure, the higher sensitivity of this "positive attitude" reagent may facilitate much deeper investigations into the quantitative proteomics of complex samples.
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Affiliation(s)
- Jean Armengaud
- CEA, DSV, IBiTec-S, SPI, Li2D, Laboratory "Innovative technologies for Detection and Diagnostics", Bagnols-sur-Cèze, France
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15
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Guzman NA, Guzman DE. An emerging micro-scale immuno-analytical diagnostic tool to see the unseen. Holding promise for precision medicine and P4 medicine. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1021:14-29. [DOI: 10.1016/j.jchromb.2015.11.026] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 11/15/2015] [Accepted: 11/17/2015] [Indexed: 01/10/2023]
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16
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Venne AS, Solari FA, Faden F, Paretti T, Dissmeyer N, Zahedi RP. An improved workflow for quantitative N-terminal charge-based fractional diagonal chromatography (ChaFRADIC) to study proteolytic events in Arabidopsis thaliana. Proteomics 2016; 15:2458-69. [PMID: 26010716 DOI: 10.1002/pmic.201500014] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 04/28/2015] [Accepted: 05/20/2015] [Indexed: 11/11/2022]
Abstract
We applied an extended charge-based fractional diagonal chromatography (ChaFRADIC) workflow to analyze the N-terminal proteome of Arabidopsis thaliana seedlings. Using iTRAQ protein labeling and a multi-enzyme digestion approach including trypsin, GluC, and subtilisin, a total of 200 μg per enzyme, and measuring only one third of each ChaFRADIC-enriched fraction by LC-MS, we quantified a total of 2791 unique N-terminal peptides corresponding to 2249 different unique N-termini from 1270 Arabidopsis proteins. Our data indicate the power, reproducibility, and sensitivity of the applied strategy that might be applicable to quantify proteolytic events from as little as 20 μg of protein per condition across up to eight different samples. Furthermore, our data clearly reflect the methionine excision dogma as well as the N-end rule degradation pathway (NERP) discriminating into a stabilizing or destabilizing function of N-terminal amino acid residues. We found bona fide NERP destabilizing residues underrepresented, and the list of neo N-termini from wild type samples may represent a helpful resource during the evaluation of NERP substrate candidates. All MS data have been deposited in the ProteomeXchange with identifier PXD001855 (http://proteomecentral.proteomexchange.org/dataset/PXD001855).
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Affiliation(s)
- A Saskia Venne
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V, Dortmund, Germany
| | - Fiorella A Solari
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V, Dortmund, Germany
| | - Frederik Faden
- Leibniz Institute of Plant Biochemistry (IPB), Halle (Saale), Germany.,ScienceCampus Halle - Plant-Based Bioeconomy, Halle (Saale), Germany
| | - Tomasso Paretti
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V, Dortmund, Germany.,Department of Molecular Medicine, Institute of Biochemistry, University of Pavia, Italy
| | - Nico Dissmeyer
- Leibniz Institute of Plant Biochemistry (IPB), Halle (Saale), Germany.,ScienceCampus Halle - Plant-Based Bioeconomy, Halle (Saale), Germany
| | - René P Zahedi
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V, Dortmund, Germany
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17
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Lee SH, Oe T. Oxidative stress-mediated N-terminal protein modifications and MS-based approaches for N-terminal proteomics. Drug Metab Pharmacokinet 2016; 31:27-34. [DOI: 10.1016/j.dmpk.2015.12.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 12/02/2015] [Accepted: 12/04/2015] [Indexed: 02/06/2023]
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18
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Locard-Paulet M, Pible O, Gonzalez de Peredo A, Alpha-Bazin B, Almunia C, Burlet-Schiltz O, Armengaud J. Clinical implications of recent advances in proteogenomics. Expert Rev Proteomics 2016; 13:185-99. [DOI: 10.1586/14789450.2016.1132169] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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19
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Gasilova N, Srzentić K, Qiao L, Liu B, Beck A, Tsybin YO, Girault HH. On-Chip Mesoporous Functionalized Magnetic Microspheres for Protein Sequencing by Extended Bottom-up Mass Spectrometry. Anal Chem 2016; 88:1775-84. [DOI: 10.1021/acs.analchem.5b04045] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Natalia Gasilova
- Laboratory
of Physical and Analytical Electrochemistry, EPFL Valais, Ecole Polytechnique Fédérale de Lausanne, 1951 Sion, Valais, Switzerland
| | - Kristina Srzentić
- Biomolecular
Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Vaud, Switzerland
| | - Liang Qiao
- Laboratory
of Physical and Analytical Electrochemistry, EPFL Valais, Ecole Polytechnique Fédérale de Lausanne, 1951 Sion, Valais, Switzerland
| | - Baohong Liu
- Department
of Chemistry and Institute of Biomedical Sciences, Fudan University, Shanghai 200433, PR China
| | - Alain Beck
- Centre d’Immunologie
Pierre Fabre, 74160 St. Julien-en-Genevois, France
| | - Yury O. Tsybin
- Spectroswiss Sàrl, EPFL Innovation Park, 1015 Lausanne, Vaud, Switzerland
| | - Hubert H. Girault
- Laboratory
of Physical and Analytical Electrochemistry, EPFL Valais, Ecole Polytechnique Fédérale de Lausanne, 1951 Sion, Valais, Switzerland
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20
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Mayne J, Ning Z, Zhang X, Starr AE, Chen R, Deeke S, Chiang CK, Xu B, Wen M, Cheng K, Seebun D, Star A, Moore JI, Figeys D. Bottom-Up Proteomics (2013-2015): Keeping up in the Era of Systems Biology. Anal Chem 2015; 88:95-121. [PMID: 26558748 DOI: 10.1021/acs.analchem.5b04230] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Janice Mayne
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Zhibin Ning
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Xu Zhang
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Amanda E Starr
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Rui Chen
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Shelley Deeke
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Cheng-Kang Chiang
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Bo Xu
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Ming Wen
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Kai Cheng
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Deeptee Seebun
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Alexandra Star
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Jasmine I Moore
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
| | - Daniel Figeys
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Rd., Ottawa, Ontario, Canada , K1H8M5
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21
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Berry IJ, Steele JR, Padula MP, Djordjevic SP. The application of terminomics for the identification of protein start sites and proteoforms in bacteria. Proteomics 2015; 16:257-72. [DOI: 10.1002/pmic.201500319] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 09/21/2015] [Accepted: 09/30/2015] [Indexed: 01/11/2023]
Affiliation(s)
- Iain J. Berry
- The ithree Institute; University of Technology Sydney; Broadway NSW Australia
- Proteomics Core Facility; University of Technology Sydney; Broadway NSW Australia
| | - Joel R. Steele
- Proteomics Core Facility; University of Technology Sydney; Broadway NSW Australia
| | - Matthew P. Padula
- The ithree Institute; University of Technology Sydney; Broadway NSW Australia
- Proteomics Core Facility; University of Technology Sydney; Broadway NSW Australia
| | - Steven P. Djordjevic
- The ithree Institute; University of Technology Sydney; Broadway NSW Australia
- Proteomics Core Facility; University of Technology Sydney; Broadway NSW Australia
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22
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Christie-Oleza JA, Armengaud J. Proteomics of theRoseobacterclade, a window to the marine microbiology landscape. Proteomics 2015; 15:3928-42. [DOI: 10.1002/pmic.201500222] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 08/24/2015] [Accepted: 09/22/2015] [Indexed: 11/07/2022]
Affiliation(s)
| | - Jean Armengaud
- CEA; DSV; IBiTec-S; SPI; Li2D; Laboratory “Innovative Technologies for Detection and Diagnostics”; Bagnols-sur-Cèze France
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23
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Li L, Wu R, Yan G, Gao M, Deng C, Zhang X. A novel method to isolate protein N-terminal peptides from proteome samples using sulfydryl tagging and gold-nanoparticle-based depletion. Anal Bioanal Chem 2015; 408:441-8. [DOI: 10.1007/s00216-015-9136-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 10/15/2015] [Accepted: 10/20/2015] [Indexed: 12/18/2022]
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24
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Li L, Yan G, Zhang X. Isolation of acetylated and free N-terminal peptides from proteomic samples based on tresyl-functionalized microspheres. Talanta 2015; 144:122-8. [DOI: 10.1016/j.talanta.2015.05.068] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2015] [Revised: 05/21/2015] [Accepted: 05/25/2015] [Indexed: 12/26/2022]
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25
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Pible O, Armengaud J. Improving the quality of genome, protein sequence, and taxonomy databases: A prerequisite for microbiome meta-omics 2.0. Proteomics 2015; 15:3418-23. [DOI: 10.1002/pmic.201500104] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Revised: 04/17/2015] [Accepted: 05/30/2015] [Indexed: 01/27/2023]
Affiliation(s)
- Olivier Pible
- CEA-Marcoule, DSV/IBITEC-S/SPI/Li2D; Laboratory “Innovative technologies for Detection and Diagnostics”; Bagnols-sur-Cèze France
| | - Jean Armengaud
- CEA-Marcoule, DSV/IBITEC-S/SPI/Li2D; Laboratory “Innovative technologies for Detection and Diagnostics”; Bagnols-sur-Cèze France
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26
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Shen H, An M, Zou X, Zhao X, Wang Q, Xing G, Ji J. Evaluation of the accuracy of protein quantification using isotope TMPP-labeled peptides. Proteomics 2015; 15:2903-9. [DOI: 10.1002/pmic.201400495] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Revised: 03/12/2015] [Accepted: 04/28/2015] [Indexed: 01/13/2023]
Affiliation(s)
- Hongyan Shen
- State Key Laboratory of Protein and Plant Gene Research; College of Life Sciences; Peking University; Beijing P. R. China
| | - Mingrui An
- State Key Laboratory of Protein and Plant Gene Research; College of Life Sciences; Peking University; Beijing P. R. China
| | - Xiao Zou
- State Key Laboratory of Protein and Plant Gene Research; College of Life Sciences; Peking University; Beijing P. R. China
| | - Xuyang Zhao
- State Key Laboratory of Protein and Plant Gene Research; College of Life Sciences; Peking University; Beijing P. R. China
| | - Qingsong Wang
- State Key Laboratory of Protein and Plant Gene Research; College of Life Sciences; Peking University; Beijing P. R. China
| | - Guowen Xing
- Institute of Organic Chemistry; College of Chemistry; Beijing Normal University; Beijing P. R. China
| | - Jianguo Ji
- State Key Laboratory of Protein and Plant Gene Research; College of Life Sciences; Peking University; Beijing P. R. China
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27
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Kucharova V, Wiker HG. Proteogenomics in microbiology: taking the right turn at the junction of genomics and proteomics. Proteomics 2014; 14:2360-675. [PMID: 25263021 DOI: 10.1002/pmic.201400168] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 08/18/2014] [Accepted: 09/23/2014] [Indexed: 12/14/2022]
Abstract
High-accuracy and high-throughput proteomic methods have completely changed the way we can identify and characterize proteins. MS-based proteomics can now provide a unique supplement to genomic data and add a new level of information to the interpretation of genomic sequences. Proteomics-driven genome annotation has become especially relevant in microbiology where genomes are sequenced on a daily basis and limitations of an in silico driven annotation process are well recognized. In this review paper, we outline different strategies on how one can design a proteogenomic experiment, for example on genome-sequenced (synonymous proteogenomics) versus unsequenced organisms (ortho-proteogenomics) or with the aid of other "omic" data such as RNA-seq. We touch upon many challenges that are encountered during a typical proteogenomic study, mostly concerning bioinformatics methods and downstream data analysis, but also related to creation and use of sequence databases. A large list of proteogenomic case studies of different microorganisms is provided to illustrate the mapping of MS/MS-derived peptide spectra to genomic DNA sequences. These investigations have led to accurate determination of translational initiation sites, pointed out eventual read-throughs or programmed frameshifts, detected signal peptide processing or other protein maturation events, removed questionable annotation assignments, and provided evidence for predicted hypothetical proteins.
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Affiliation(s)
- Veronika Kucharova
- Department of Clinical Science, The Gade Research Group for Infection and Immunity, University of Bergen, Norway
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28
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Hartmann EM, Armengaud J. N-terminomics and proteogenomics, getting off to a good start. Proteomics 2014; 14:2637-46. [PMID: 25116052 DOI: 10.1002/pmic.201400157] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 04/23/2014] [Accepted: 08/08/2014] [Indexed: 12/11/2022]
Abstract
Proteogenomics consists of the annotation or reannotation of protein-coding nucleic acid sequences based on the empirical observation of their gene products. While functional annotation of predicted genes is increasingly feasible given the multiplicity of genomes available for many branches of the tree of life, the accurate annotation of the translational start sites is still a point of contention. Extensive coverage of the proteome, including specifically the N-termini, is now possible, thanks to next-generation mass spectrometers able to record data from thousands of proteins at once. Efforts to increase the peptide coverage of protein sequences and to detect low abundance proteins are important to make proteomic and proteogenomic studies more comprehensive. In this review, we present the panoply of N-terminus-oriented strategies that have been developed over the last decade.
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Affiliation(s)
- Erica M Hartmann
- Biology and the Built Environment Center, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
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29
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Durighello E, Christie-Oleza JA, Armengaud J. Assessing the exoproteome of marine bacteria, lesson from a RTX-toxin abundantly secreted by Phaeobacter strain DSM 17395. PLoS One 2014; 9:e89691. [PMID: 24586966 PMCID: PMC3933643 DOI: 10.1371/journal.pone.0089691] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 01/21/2014] [Indexed: 11/24/2022] Open
Abstract
Bacteria from the Roseobacter clade are abundant in surface marine ecosystems as over 10% of bacterial cells in the open ocean and 20% in coastal waters belong to this group. In order to document how these marine bacteria interact with their environment, we analyzed the exoproteome of Phaeobacter strain DSM 17395. We grew the strain in marine medium, collected the exoproteome and catalogued its content with high-throughput nanoLC-MS/MS shotgun proteomics. The major component represented 60% of the total protein content but was refractory to either classical proteomic identification or proteogenomics. We de novo sequenced this abundant protein with high-resolution tandem mass spectra which turned out being the 53 kDa RTX-toxin ZP_02147451. It comprised a peptidase M10 serralysin domain. We explained its recalcitrance to trypsin proteolysis and proteomic identification by its unusual low number of basic residues. We found this is a conserved trait in RTX-toxins from Roseobacter strains which probably explains their persistence in the harsh conditions around bacteria. Comprehensive analysis of exoproteomes from environmental bacteria should take into account this proteolytic recalcitrance.
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Affiliation(s)
- Emie Durighello
- CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze, France
| | | | - Jean Armengaud
- CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze, France
- * E-mail:
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30
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Armengaud J, Trapp J, Pible O, Geffard O, Chaumot A, Hartmann EM. Non-model organisms, a species endangered by proteogenomics. J Proteomics 2014; 105:5-18. [PMID: 24440519 DOI: 10.1016/j.jprot.2014.01.007] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 12/24/2013] [Accepted: 01/07/2014] [Indexed: 10/25/2022]
Abstract
UNLABELLED Previously, large-scale proteomics was possible only for organisms whose genomes were sequenced, meaning the most common model organisms. The use of next-generation sequencers is now changing the deal. With "proteogenomics", the use of experimental proteomics data to refine genome annotations, a higher integration of omics data is gaining ground. By extension, combining genomic and proteomic data is becoming routine in many research projects. "Proteogenomic"-flavored approaches are currently expanding, enabling the molecular studies of non-model organisms at an unprecedented depth. Today draft genomes can be obtained using next-generation sequencers in a rather straightforward way and at a reasonable cost for any organism. Unfinished genome sequences can be used to interpret tandem mass spectrometry proteomics data without the need for time-consuming genome annotation, and the use of RNA-seq to establish nucleotide sequences that are directly translated into protein sequences appears promising. There are, however, certain drawbacks that deserve further attention for RNA-seq to become more efficient. Here, we discuss the opportunities of working with non-model organisms, the proteomic methods that have been used until now, and the dramatic improvements proffered by proteogenomics. These put the distinction between model and non-model organisms in great danger, at least in terms of proteomics! BIOLOGICAL SIGNIFICANCE Model organisms have been crucial for in-depth analysis of cellular and molecular processes of life. Focusing the efforts of thousands of researchers on the Escherichia coli bacterium, Saccharomyces cerevisiae yeast, Arabidopsis thaliana plant, Danio rerio fish and other models for which genetic manipulation was possible was certainly worthwhile in terms of fundamental and invaluable biological insights. Until recently, proteomics of non-model organisms was limited to tedious, homology-based techniques, but today draft genomes or RNA-seq data can be straightforwardly obtained using next-generation sequencers, allowing the establishment of a draft protein database for any organism. Thus, proteogenomics opens new perspectives for molecular studies of non-model organisms, although they are still difficult experimental organisms. This article is part of a Special Issue entitled: Proteomics of non-model organisms.
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Affiliation(s)
- Jean Armengaud
- CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze F-30207, France.
| | - Judith Trapp
- CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze F-30207, France; Irstea, UR MALY, F-69626 Villeurbanne, France
| | - Olivier Pible
- CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze F-30207, France
| | | | | | - Erica M Hartmann
- CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze F-30207, France
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